INFOBIOMED UA/IEETA - Recent Activities

1. INFOBIOMEDUA/IEETA - Recent Activities 10th Consortium Meeting Girona, February 12-13, 2007 José Luis Oliveira

2. Technical Work • DIA software • Digital Analysis of Dental X-Ray Images • Extraction of the tooth contours • Microarray information systems • MIND • GPX • DiseaseCard • Integration of genetic and medical information for Rare Diseases

3. DIA - Digital Analysis of Dental X-Ray • Main Goals • To evaluate the performance of the image analysis methods for extracting morphologic data, from dental x-ray images; • To develop a program and a friendly interface for the proposed methodologies; • To implement a database for clinical information. • Collaboration • ACTA (NL)

4. Past Work • Algorithms to extract the tooth contours (segmentation); • Patients database; • Bone Loss evaluation starting from the tooth contours; • Study the variability of bone loss measures done by hand against the software results. • Authentication mechanism • A new algorithm to extract the tooth contours, in particular the root contour • based on the live-wire paradigm • New Database Model • and migration to SQL Server • Data exchange with ACTA databases • New software prototype

5. Recent Work • Website • http://www.ieeta.pt/dia • Meeting in Amsterdam (October, 16-20) • (under conclusion) a statistical study • To analyze the agreement between users, and • To evaluate if there are significant differences between the measures done by the software and the measures made by hand. • The measures are currently being performed in ACTA • Software improvements • Graphical organization and on usability • Following the suggestions of ACTA partners

6. Main Results • Extraction of tooth contour from most of the dental x-ray images; • Quantitative properties of the teeth (eg. Bone Loss) can be estimated; • This system can be used as an auxiliary tool in the diagnosis of several pathologies, such as the periodontitis; • The results of analysis of dental x-ray images can be stored in a database; • This tool can also be used to visualize the report of bone loss measurements (organized by date) and to evaluate its evolution (disease history); • This tool can be used as an organizer of dental X-Ray images of the patients; • The storage process on the database assures the diagnostic quality of the images.

7. Future Work • Dental image co-registration • Development of a few administrative tools • Create users, change passwords, … • Software manuals • Publications • Dissemination

8. Microarrays I.S. - GPX Main goal: Implementation of a microarray data submission pipeline into the ArrayExpress Collaboration: ScGTI (UK) Details: • Mapping of the GPX database into the MAGE standard; • Interaction with the EBI to validate the developed work; • Implementation of an application to retrieve the data from the GPX database and produce the MAGE-ML

9. Microarrays I.S. - mind Main goal: Implementation of a Web-based public microarray database Collaboration: ISCIII (SP) Details: “... focus on the way the microarray data is acquired, stored, analysed and exchanged.” Main caracteristics: • Public microarray LIMS • Integration of data analysis • Quality control + Exploratory analysis • Compliant with the MGED standards • MIAME and MAGE • Currently at: • http://bioinformatics.ua.pt/mind

10. Mind Architecture Data storage Data analysis Data mining tools LIMS Exploratory analysis public repository MIND Quality control Diseasecard integration MAGE adaptor Database integration Systems integration Data exchange

11. Mind workflow The complete set of bioassays (hybridizations) and their descriptions performed as an experiment for a common purpose. An experiment will be often equivalent to a publication. Through the MAGE-TAB format an experiment can be imported or exported. Description of the processing state of the biomaterial for use in the microarray hybridization. Gene Expression output data Data analysis tools Documentation of the set of steps taken in a procedure. MAGE package that describes the array layout and design.

12. bioinformatics.ua.pt/mind

13. DiseaseCard • Main Goal • Integration of heterogeneous and distributed genetic and clinical databases, under a common appearance and navigation method. • Focus on Rare Diseases • ~ 6,000 distinct rare diseases • 6% to 8% of the population • Between 24-36 M of citizens in EC. • Collaborations • ISCIII (SP)

14. Navigation Protocol

15. User Interface

16. User Interface

17. Recent Work • Integration of WEB 2.0 features • AJAX interfaces • Synonyms and abbreviations • Search disease by abbreviations; • example: Aarskog-Scott syndrome FGDY • Forums

18. Ajax

19. Synonyms

20. Forums • Goals: • Facilitate the sharing of information between Researchers and the Community. • Enlarge the knowledge of the DiseaseCard portal. • Create a discussion point over the portal. • Allows: • Posting information for a specific disease or for the portal • Implies users’ registration • Easy edition (text/html) • insertion of images and links to other websites.

21. Forums

22. Ongoing • Introduction of new Databases on the Extraction protocol; • Development of a Management System; • Statistical Analysis of the Extraction Protocol penetration; Ideas are welcome!! 

23. Dissemination • Conference organization • National Congress of Biochemistry • Equipment Exhibition (near 30 enterprises) • December, 8-10 • ~650 participants • http://www.ieeta.pt/ncb2006

24. INFOBIOMEDUA/IEETA - Recent Activities 10th Consortium Meeting Girona, February 12-13, 2007 José Luis Oliveira